Since there doesn't seem to be an announcement thread for VVVVVV, I'm going to have to go ahead and recommend it. I love the game.
Software wise, although I could name a truckload of apps, I'll throw down an unknown- Liquid Story Binder XE. It's a bit quirky in a few places, but really helpful if you're looking to collate a whole lot of random info. It's also the cheapest program around to build storyboards.